Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors.

The hypothesis that the evolution of humans involves hybridization between diverged species has been actively debated in recent years. We present the following novel evidence in support of this hypothesis: the analysis of nuclear pseudogenes of mtDNA ("NUMTs"). NUMTs are considered "mtDNA fossils" as they preserve sequences of ancient mtDNA and thus carry unique information about ancestral populations. Our comparison of a NUMT sequence shared by humans, chimpanzees, and gorillas with their mtDNAs implies that, around the time of divergence between humans and chimpanzees, our evolutionary history involved the interbreeding of individuals whose mtDNA had diverged as much as ~4.5 Myr prior. This large divergence suggests a distant interspecies hybridization. Additionally, analysis of two other NUMTs suggests that such events occur repeatedly. Our findings suggest a complex pattern of speciation in primate/human ancestors and provide one potential explanation for the mosaic nature of fossil morphology found at the emergence of the hominin lineage. A preliminary version of this manuscript was uploaded to the preprint server BioRxiv in 2017 (10.1101/134502).

MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses.

Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase ( www.facebase.org , https://doi.org/10.25550/3-HXMC ) and GitHub ( https://github.com/jaydevine/MusMorph ).

Hybridization in human evolution: Insights from other organisms.

During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arising from these dynamics and the environmental conditions under which it occurs. Here we draw from our collective research across various organisms, illustrating some of the ways in which gene exchange can structure genomic/phenotypic diversity within/among species. We present a range of examples relevant to questions about the evolution of hominins. These examples are not meant to be exhaustive, but rather illustrative of the diverse evolutionary causes/consequences of hybridization, highlighting potential drivers of human evolution in the context of hybridization including: influences on adaptive evolution, climate change, developmental systems, sex-differences in behavior, Haldane's rule and the large X-effect, and transgressive phenotypic variation.

Data on the time of integration of the human mitochondrial pseudogenes (NUMTs) into the nuclear genome.

The data and methods presented in this article are supplementing the research article "Integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A hypothesis", DOI: 10.1016/j.mito.2016.12.001 (Gunbin et al., 2017) [1]. Mitochondrial DNA is known to get inserted into nuclear DNA to form NUMTs, i.e. nuclear DNA pseudogenes of the mtDNA. We present here the sequences of selected NUMTs, in which time of integration can be determined with sufficient precision. We report their chromosomal positions , their position within the great ape mtDNA phylogeny, and their times of integration into the nuclear genome. The methods used to generate the data and to control their quality are also presented. The dataset is made publicly available to enable critical or extended analyzes.

Integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A hypothesis.

Fragments of mitochondrial DNA are known to get inserted into nuclear DNA to form NUMTs, i.e. nuclear pseudogenes of the mtDNA. The insertion of a NUMT is a rare event. Hundreds of pseudogenes have been cataloged in the human genome. NUMTs are, in essence, a special type of mutation with their own internal timer, which is synchronized with an established molecular clock, the mtDNA. Thus insertion of NUMTs can be timed with respect to evolution milestones such as the emergence of new species. We asked whether NUMTs were inserted uniformly over time or preferentially during certain periods of evolution, as implied by the "punctuated evolution" model. To our surprise, the NUMT insertion times do appear nonrandom with at least one cluster positioned at around 2.8 million years ago (Ma). Interestingly, 2.8Ma closely corresponds to the time of emergence of the genus Homo, and to a well-documented period of major climate change ca. 2.9-2.5Ma. It is tempting to hypothesize that the insertion of NUMTs is related to the speciation process. NUMTs could be either "riders", i.e., their insertion could be facilitated by the overall higher genome rearrangement activity during speciation, or "drivers", i.e. they may more readily get fixed in the population due to positive selection associated with speciation. If correct, the hypothesis would support the idea that evolution of our genus may have happened in a rapid, punctuated manner.

Skull diversity in the Homo lineage and the relative position of Homo naledi.

The discovery of Homo naledi has expanded the range of phenotypic variation in Homo, leading to new questions surrounding the mosaic nature of morphological evolution. Though currently undated, its unique morphological pattern and possible phylogenetic relationships to other hominin taxa suggest a complex evolutionary scenario. Here, we perform geometric morphometric analyses on H. naledi cranial and mandibular remains to investigate its morphological relationship with species of Homo and Australopithecus. We use Generalized Procrustes analysis to place H. naledi within the pattern of known hominin skull diversity, distributions of Procrustes distances among individuals to compare H. naledi and Homo erectus, and neighbor joining trees to investigate the potential phenetic relationships between groups. Our goal is to address a set of hypotheses relating to the uniqueness of H. naledi, its affinity with H. erectus, and the age of the fossils based on skull morphology. Our results indicate that, cranially, H. naledi aligns with members of the genus Homo, with closest affiliations to H. erectus. The mandibular results are less clear; H. naledi closely associates with a number of taxa, including some australopiths. However, results also show that although H. naledi shares similarities with H. erectus, some distances from this taxon - especially small-brained members of this taxon - are extreme. The neighbor joining trees place H. naledi firmly within Homo. The trees based on cranial morphology again indicate a close relationship between H. naledi and H. erectus, whereas the mandibular tree places H. naledi closer to basal Homo, suggesting a deeper antiquity. Altogether, these results emphasize the unique combination of features (H. erectus-like cranium, less derived mandible) defining H. naledi. Our results also highlight the variability within Homo, calling for a greater focus on the cause of this variability, and emphasizing the importance of using the total morphological package for species diagnoses.

The skull of Homo naledi.

The species Homo naledi was recently named from specimens recovered from the Dinaledi Chamber of the Rising Star cave system in South Africa. This large skeletal sample lacks associated faunal material and currently does not have a known chronological context. In this paper, we present comprehensive descriptions and metric comparisons of the recovered cranial and mandibular material. We describe 41 elements attributed to Dinaledi Hominin (DH1-DH5) individuals and paratype U.W. 101-377, and 32 additional cranial fragments. The H. naledi material was compared to Plio-Pleistocene fossil hominins using qualitative and quantitative analyses including over 100 linear measurements and ratios. We find that the Dinaledi cranial sample represents an anatomically homogeneous population that expands the range of morphological variation attributable to the genus Homo. Despite a relatively small cranial capacity that is within the range of australopiths and a few specimens of early Homo, H. naledi shares cranial characters with species across the genus Homo, including Homo habilis, Homo rudolfensis, Homo erectus, and Middle Pleistocene Homo. These include aspects of cranial form, facial morphology, and mandibular anatomy. However, the skull of H. naledi is readily distinguishable from existing species of Homo in both qualitative and quantitative assessments. Since H. naledi is currently undated, we discuss the evolutionary implications of its cranial morphology in a range of chronological frameworks. Finally, we designate a sixth Dinaledi Hominin (DH6) individual based on a juvenile mandible.

The evolutionary relationships and age of Homo naledi: An assessment using dated Bayesian phylogenetic methods.

Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: "Where does H. naledi fit in the hominin evolutionary tree?" and "How old is it?" We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out three analyses. First, we performed a dated Bayesian analysis to generate estimates of the evolutionary relationships of fossil hominins including H. naledi. Then we employed Bayes factor tests to compare the strength of support for hypotheses about the relationships of H. naledi suggested by the best-estimate trees. Lastly, we carried out a resampling analysis to assess the accuracy of the age estimate for H. naledi yielded by the dated Bayesian analysis. The analyses strongly supported the hypothesis that H. naledi forms a clade with the other Homo species and Australopithecus sediba. The analyses were more ambiguous regarding the position of H. naledi within the (Homo, Au. sediba) clade. A number of hypotheses were rejected, but several others were not. Based on the available craniodental data, Homo antecessor, Asian Homo erectus, Homo habilis, Homo floresiensis, Homo sapiens, and Au. sediba could all be the sister taxon of H. naledi. According to the dated Bayesian analysis, the most likely age for H. naledi is 912 ka. This age estimate was supported by the resampling analysis. Our findings have a number of implications. Most notably, they support the assignment of the new specimens to Homo, cast doubt on the claim that H. naledi is simply a variant of H. erectus, and suggest H. naledi is younger than has been previously proposed.

Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa.

Homo naledi is a previously-unknown species of extinct hominin discovered within the Dinaledi Chamber of the Rising Star cave system, Cradle of Humankind, South Africa. This species is characterized by body mass and stature similar to small-bodied human populations but a small endocranial volume similar to australopiths. Cranial morphology of H. naledi is unique, but most similar to early Homo species including Homo erectus, Homo habilis or Homo rudolfensis. While primitive, the dentition is generally small and simple in occlusal morphology. H. naledi has humanlike manipulatory adaptations of the hand and wrist. It also exhibits a humanlike foot and lower limb. These humanlike aspects are contrasted in the postcrania with a more primitive or australopith-like trunk, shoulder, pelvis and proximal femur. Representing at least 15 individuals with most skeletal elements repeated multiple times, this is the largest assemblage of a single species of hominins yet discovered in Africa.

Characterizing the evolutionary path(s) to early Homo.

Numerous studies suggest that the transition from Australopithecus to Homo was characterized by evolutionary innovation, resulting in the emergence and coexistence of a diversity of forms. However, the evolutionary processes necessary to drive such a transition have not been examined. Here, we apply statistical tests developed from quantitative evolutionary theory to assess whether morphological differences among late australopith and early Homo species in Africa have been shaped by natural selection. Where selection is demonstrated, we identify aspects of morphology that were most likely under selective pressure, and determine the nature (type, rate) of that selection. Results demonstrate that selection must be invoked to explain an Au. africanus-Au. sediba-Homo transition, while transitions from late australopiths to various early Homo species that exclude Au. sediba can be achieved through drift alone. Rate tests indicate that selection is largely directional, acting to rapidly differentiate these taxa. Reconstructions of patterns of directional selection needed to drive the Au. africanus-Au. sediba-Homo transition suggest that selection would have affected all regions of the skull. These results may indicate that an evolutionary path to Homo without Au. sediba is the simpler path and/or provide evidence that this pathway involved more reliance on cultural adaptations to cope with environmental change.

Further evidence for phenotypic signatures of hybridization in descendant baboon populations.

Hybridization may have played a substantial role in shaping the diversity of our evolving lineage. Although recent genomic evidence has shown that hybridization occurred between anatomically modern humans (AMHS) and Neanderthals, it remains difficult to pin down precisely where and when this gene flow took place. Investigations of the hybrid phenotype in primates and other mammals are providing models for identifying signatures of hybridization in the fossil record. However, our understanding of intra- and inter-taxon variation in hybrids is still limited. Moreover, there is little evidence from these studies that is pertinent to the question of how long hybrid skeletal traits persist in descendants, and therefore it is not clear whether observed hybrid phenotypes are evidence of recent (e.g., F1) or much earlier hybridization events. Here, we present an analysis updating a previous study of cranial variation in pedigreed olive and yellow baboons and their hybrids. Results suggest that traits previously associated with hybrids in baboons and other mammalian species are also present in this expanded data set; many of these traits are highly heritable, confirming a genetic basis for their variation in this mixed population. While F1 animals - and especially F1 males - still have the highest number of dental anomalies, these and other atypical traits persist into later hybrid generations (such as F2 and B1). Moreover, non-F1 recombinants also show extremely rare trait variations, including reduced canines and rotated teeth. However, these results must be considered in light of the possibility that some founding individuals may have themselves been unrecognized hybrids. Despite this, the data are compelling, and indicate once again that further controlled research remains to be done on primates and other mammals in order to better understand variation in the hybrid phenotype.

Mandibular remains support taxonomic validity of Australopithecus sediba.

Since the announcement of the species Australopithecus sediba, questions have been raised over whether the Malapa fossils represent a valid taxon or whether inadequate allowance was made for intraspecific variation, in particular with reference to the temporally and geographically proximate species Au. africanus. The morphology of mandibular remains of Au. sediba, including newly recovered material discussed here, shows that it is not merely a late-surviving morph of Au. africanus. Rather-as is seen elsewhere in the cranium, dentition, and postcranial skeleton-these mandibular remains share similarities with other australopiths but can be differentiated from the hypodigm of Au. africanus in both size and shape as well as in their ontogenetic growth trajectory.

Craniofacial variation and developmental divergence in primate and human evolution.

Many questions about developmental divergence in human (and non-human primate) evolution can be fruitfully explored through investigation of the extant primate phenotype. Here I discuss two approaches that use patterns of variation in extant primates to consider hypotheses of 'tinkering' both in their own lineages, and also as applied to the fossil record of human evolution. In the first, I show how comparisons of ontogenetic morphological integration in extant humans and apes can be used to consider the developmental underpinnings of the morphological change seen in the transition from the prognathic australopith face to the relatively smaller, orthognathic Homo face. In the second approach, I demonstrate how studies of craniofacial variation in hybrid baboons can be used as models for considering developmental divergence in Plio-Pleistocene primates, including fossil hominins. Of particular interest is the fact that unusual non-metric dental and sutural variation in these hybrids appears to be a sensitive indicator of evolutionary developmental divergence. Future studies would profit from focusing on the breadth and especially the overlap of morphological variation among extant primate taxa in order to determine the degree to which underlying genetic similarity in functional regions, and difference in regulatory regions, explains the variable primate phenotype.